GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocE in Rhodococcus qingshengii djl-6-2

Align Amino-acid permease RocE (characterized)
to candidate WP_003943879.1 C1M55_RS01060 amino acid permease

Query= SwissProt::P39137
         (467 letters)



>NCBI__GCF_002893965.1:WP_003943879.1
          Length = 469

 Score =  305 bits (780), Expect = 3e-87
 Identities = 156/403 (38%), Positives = 246/403 (61%), Gaps = 8/403 (1%)

Query: 11  LQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCLGEL 70
           LQ T+K RHL MI++ GVIG G F+G+G  I + GP G ++SY + G ++ L M  LGE+
Sbjct: 9   LQHTLKKRHLSMIAIAGVIGAGLFVGSGVAIQETGP-GVLISYALAGVVVILVMRMLGEM 67

Query: 71  AVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHIDVWI 130
           + A P +GSF +YA K I    GF+ GWLY   W +   IE  +   +M RW P +  W 
Sbjct: 68  SAASPETGSFSSYADKAIGRWAGFSIGWLYAWFWIIVLGIEATAGALIMNRWVPGVPQWT 127

Query: 131 WCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKGGEQAPF 190
           W L+   ++ + N I+ K+F E EFWF+ IK++ I+ F+ +G  A+ G +    G +AP 
Sbjct: 128 WALILMIVLTLTNIISVKSFGEFEFWFASIKVVAIIAFLGMGIVAICGWMP---GVEAPG 184

Query: 191 LTHFYEDGLF-PNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVWRT 249
           +T+    G F PNG  AML  ++ V F+F G E+  +AAGES +P + +  ++K  VWR 
Sbjct: 185 MTNLTGHGGFLPNGTGAMLAAVLVVVFSFFGAEIATIAAGESANPLEAVRAAVKSVVWRI 244

Query: 250 LVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVANSGLY 309
           L+F++ SI V+  ++PW  A V  SP+VAV +  GIP A +IM+ V+L ++LS  NSGLY
Sbjct: 245 LIFYIGSIAVVVTLLPWDSASVALSPYVAVMDSYGIPAAGNIMDVVVLTSVLSCLNSGLY 304

Query: 310 ASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVYMVLLSL 369
            ++R+++++A  G A K+L +  + GVPM +++V+  V  L++   +   + V++ L++ 
Sbjct: 305 TASRMIFSLAGRGDAPKSLSRIEKTGVPMRAVLVSTIVGFLTVGMNYLSPDKVFLFLVNS 364

Query: 370 AGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVL 412
           +G  A   W+ IS+SQ+  RRK    G   ++L+ K   +P L
Sbjct: 365 SGAIALFVWLVISVSQLRTRRKLEASG---QELELKMWFFPYL 404


Lambda     K      H
   0.329    0.142    0.438 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 498
Number of extensions: 19
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 467
Length of database: 469
Length adjustment: 33
Effective length of query: 434
Effective length of database: 436
Effective search space:   189224
Effective search space used:   189224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory